[phenixbb] To evalute the LLG value by given the structure factor information only

zhangh1 at umbc.edu zhangh1 at umbc.edu
Sat Apr 30 23:41:49 PDT 2011

Hi Pavel:

Yes, I understand it is part of phenix.refine output, but I am wondering
whether there is a way to evaluate LLG by only using user-provided
structure factor (Fo, sigFo, Fc). I think phenix.refine will have to read
a PDB file, based on which model Fc will be calculated and used to
evaluate LLG (instead of my provided Fc).

I know there is a well-established LLG formula and may write a short code
but I need to minimize sigmaA I think which take some efforts:-(

Thanks a lot!

Best Regards, Hailiang

> Hi,
> isn't it (or a simple derivative of) what phenix.refine outputs all the
> time, see log file for lines like this:
> | x-ray target function (ml) for work reflections:
> 4.379227                   |
> where ML target function is defined here:
> Acta Cryst. (1995). A51, 880-887
> Acta Cryst. (2002). A58, 270-282.
> I guess the above value is normalized by a number of reflections or
> something like this (I don't remember, but if you are interested let me
> know and I will have a look at the code). It may also not contain a
> constant part of the target.
> May be I should add it to phenix.model_vs_data output...
> Pavel.
>> Hi,
>> Is there any way in phenix (such as phenix.refine) to evaluate the
>> LLG(log-likelihood) value by given the structure factor information only
>> (Fo, sigmaFo and Fc)? Thanks in advance for any information!
>> Best regards, Hailiang
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